Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint

Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice

BACKGROUND

In hybrid rice seed production, rice varieties with a small flag leaf angle (FLA) experience obstacles to cross-pollination at the early heading stage, and farmers usually need to remove flag leaves to achieve artificial pollination. Therefore, the cultivation of rice varieties with large FLAs can not only save a substantial amount of labour in the leaf-cutting process during artificial pollination but also accelerate the mechanization of hybrid rice seed production.

RESULTS

In this study, 431 rice accessions were included in a genome-wide association study (GWAS) to identify quantitative trait loci (QTLs) and the superior haplotypes for rice FLA in 2022 and 2023. The aim of the study was to identify new QTLs and provide germplasm resources for the genetic improvement of rice FLA. The population exhibited rich phenotypic variation in FLA in both years. The FLA GWAS was performed with more than 3 million single-nucleotide polymorphisms (SNPs), and eight QTLs associated with FLA were detected; of these, six QTLs located on rice chromosomes 1, 2, 8 and 9 were novel and detected in both years. In addition, these QTLs were analysed by haplotype analysis and functional annotation, and FLA2 and FLA9, which encode xyloglucan fucosyltransferase and cytokinin-O-glucosyltransferase 2, respectively, were identified as candidate genes for FLA regulation in rice. Quantitative real-time polymerase chain reaction (qRT‒PCR) results validated FLA2 and FLA9 as candidate genes. The results of this study showed that the elite alleles of FLA2 and FLA9 can increase FLA in rice. Excellent parents for FLA improvement were predicted through pyramiding breeding.

CONCLUSIONS

A total of six new QTLs and two candidate genes (FLA2 and FLA9) were identified by a GWAS of 431 rice accessions over two years. The elite alleles and excellent parents predicted in our study can provide important information for the functional analysis of rice FLA-related genes and improvement through pyramiding breeding.

Molecular and physiological characterization of brassinosteroid receptor BRI1 mutants in Sorghum bicolor

The high sequence and structural similarities between BRASSINOSTEROID INSENSITIVE 1 (BRI1) brassinosteroid (BR) receptors of Arabidopsis (AtBRI1) and sorghum (SbBRI1) prompted us to study the functionally conserved roles of BRI1 in both organisms. Introducing sorghum SbBRI1 in Arabidopsis bri1 mutants restores defective growth and developmental phenotypes to wild-type levels. Sorghum mutants for SbBRI1 show defective BR sensitivity and impaired plant growth and development throughout the entire sorghum life cycle. Embryonic analysis of sorghum primary root techniques permits to trace back root growth and development to early stages in an unprecedented way, revealing the functionally conserved roles of the SbBRI1 receptor in BR perception during meristem development. RNA-seq analysis uncovers the downstream regulation of the SbBRI1 pathway in cell wall biogenesis during cell growth. Together, these results uncover that the sorghum SbBRI1 protein plays functionally conserved roles in plant growth and development, while encouraging the study of BR pathways in sorghum and its implications for improving resilience in cereal crops.

Genetic manipulations of brassinosteroid-related genes improve various agronomic traits and yield in cereals enabling new biotechnological revolution: Achievements and perspectives

Brassinosteroids (BRs) are steroid phytohormones which regulate various developmental and physiological processes throughout plant life cycle, from seed development and germination, up to modulation of reproduction and senescence. Importantly, mutants defective in the BR biosynthesis or response show various degree of plant height reduction (dwarfism or semi-dwarfism). This agronomic trait is of particular importance considering that in contrast to tall cereal varieties, semi-dwarf cereal plants are more tolerant to lodging which occurs during unfavorable weather conditions and constitutes a serious threat to plant reproduction and yield. Moreover, it was shown that the BR deficiency or insensitivity lead to erect stature of cereal plants what enables increase in planting density and yield. The valuable combinations of these traits make the BR-related mutants exceptional alternatives in breeding programs. Noteworthy, BRs play a noticeable role in regulation of grain/kernel shape and size. Therefore, these crucial agronomic traits may be manipulated specifically in BR-dependent manner. Importantly, the semi-dwarf mutants have been successfully introduced into cereal breeding programs in the past, and new semi-dwarf mutants developed through application of gene editing approach have been recently reported as promising alternatives for development of novel, high-yielding cereal cultivars. This review presents a comprehensive description of genetic manipulations of the BR-related genes aimed at improvements of various agronomic traits in the major cereal crops - rice, wheat, maize, and barley. These improvements may be achieved through application of panicle- or grain-specific promoters, overexpression or gain-of-function approaches, gene silencing, and targeted gene editing.

Understanding brassinosteroid-centric phytohormone interactions for crop improvement

Brassinosteroids (BRs) play a crucial role in regulating multiple biological processes in plants, particularly those related to crop productivity and stress tolerance. During their functioning, BRs engage in extensive and intricate interactions with other phytohormones, including auxin, cytokinins, gibberellins, abscisic acid, ethylene, jasmonates, salicylic acid, and strigolactones. These interactions facilitate the integration of internal and external signals, ultimately shaping the physiological status of the plant. In this review, we introduce BR metabolism and signaling and discuss their role in modulating agronomic traits that directly contribute to grain yield in rice (Oryza sativa), the model plant for crops. We also summarize recent advances in the crosstalk between BRs and other phytohormones in regulating agronomic traits in crops. Furthermore, we highlight significant research that provides insights into developing high-yielding and stress-resistant crop varieties from the perspective of hormone crosstalk. Understanding the genetic and molecular mechanisms through which BRs and other phytohormones collaboratively control agronomic traits offers new approaches for crop improvement.

LG1 promotes preligule band formation through directly activating ZmPIN1 genes in maize

Increasing plant density is an effective strategy for enhancing crop yield per unit land area. A key architectural trait for crops adapting to high planting density is a smaller leaf angle (LA). Previous studies have demonstrated that LG1, a SQUAMOSA BINDING PROTEIN (SBP) transcription factor, plays a critical role in LA establishment. However, the molecular mechanisms underlying the regulation of LG1 on LA formation remain largely unclear. In this study, we conduct comparative RNA-seq analysis of the preligule band (PLB) region of wild type and lg1 mutant leaves. Gene Ontology (GO) term enrichment analysis reveals enrichment of phytohormone pathways and transcription factors, including three auxin transporter genes ZmPIN1a, ZmPIN1b, and ZmPIN1c. Further molecular experiments demonstrate that LG1 can directly bind to the promoter region of these auxin transporter genes and activate their transcription. We also show that double and triple mutants of these ZmPINs genes exhibit varying degrees of auricle size reduction and thus decreased LA. On the contrary, overexpression of ZmPIN1a causes larger auricle and LA. Taken together, our findings establish a functional link between LG1 and auxin transport in regulating PLB formation and provide valuable targets for genetic improvement of LA for breeding high-density tolerant maize cultivars.

NcBRI1 positively regulate vascular development and promote biomass production in Neolamarckia cadamba

Brassinosteroids (BRs) are essential phytohormones that play a crucial role in plant growth and development. However, our understanding of BR receptors and their functions in tree species is currently limited. In this study, we looked for potential BR receptor genes in the burflower-tree (Neolamarckia cadamba) genome. We identified five candidate gene from sequence analysis and phylogenetic reconstruction. Among these genes, Neolamarckia cadamba BRASSINOSTEROID-INSENSITIVE 1 (NcBRI1) is ubiquitously expressed in all tested tissues and encodes a functional BR receptor localized to the plasma membrane. Ectopic expression of NcBRI1 in the Arabidopsis (Arabidopsis thaliana) loss-of-function BRI1 mutant bri1-5 not only rescued its growth retardation phenotype but also facilitated vascular development by reactivating BR signal transduction. Furthermore, overexpression of NcBRI1 promoted vascular formation and cell elongation in transgenic hairy roots of Neolamarckia cadamba. By contrast, microRNA-mediated knockdown of NcBRI1 resulted in delayed vascular development and smaller cells. Importantly, we found that manipulation of NcBRI1 in Neolamarckia cadamba can enhance the biomass of hairy roots. These findings highlight the critical role of NcBRI1 in BR signaling and its significant influence on vascular development and rapid growth in Neolamarckia cadamba.

OsMAPKKK5 affects brassinosteroid signal transduction via phosphorylating OsBSK1-1 and regulates rice plant architecture and yield

Improving plant architecture and increasing yields are the main goals of rice breeders. However, yield is a complex trait influenced by many yield-related traits. Identifying and characterizing important genes in the coordinated network regulating complex rice traits and their interactions is conducive to cultivating high-yielding rice varieties. In this study, we determined that the interaction between mitogen-activated protein kinase kinase kinase5 (OsMAPKKK5) and brassinosteroid-signalling kinase1-1 (OsBSK1-1) regulates yield-related traits in rice. Specifically, OsMAPKKK5 phosphorylates OsBSK1-1, which enhances the interaction between these two proteins, but adversely affects the OsBSK1-1-OsBRI1 (BR insensitive1) and OsBSK1-1-OsPPKL1 (protein phosphatase with two Kelch-like domains) interactions. Additionally, OsMAPKKK5 disrupts brassinosteroid signal transduction, which prevents OsBZR1 (brassinazole-resistant1) from efficiently entering the nucleus, thereby negatively modulating its function as a transcription factor regulating downstream effector genes, ultimately adversely affecting plant architecture and yield. This study revealed the relationship between the MAPK cascade and the regulatory effects of brassinosteroid on the rice grain yield involves OsMAPKKK5 and OsBSK1-1. The study data may be important for future investigations on the rice yield-regulating molecular network.

SMALL AND ROUND GRAIN is involved in the brassinosteroid signaling pathway which regulates grain size in rice

Grain size is a key determinant of 1,000-grain weight, one of three factors determining grain yield. However, the complete regulatory network controlling grain size has not been fully clarified. Here, we identified a rice mutant, named small and round grain (srg) that exhibits semi-dwarf stature and small grain size. Cytological analysis showed that cell length and number of spikelet epidermal cells of the srg mutant are reduced, indicating that SRG controls grain size by promoting cell elongation and increasing cell number. SRG encodes a kinesin belonging to the kinesin-1 subfamily and is extensively expressed in different plant tissues with relatively high expression in young panicles. SRG protein is mainly located in the nucleus and cell membrane. Expression of the SRG gene was induced by brassinolide through the brassinosteroid (BR) responsive factor OsWRKY53 and SRG protein was phosphorylated by BR-activated kinase OsBSK3 to prevent its degradation. In addition, microtubule (MT) morphology was abnormal and disordered in the srg and cr-1 mutants. These findings suggest that BR likely stabilizes orderly assembly and arrangement of MTs by stabilizing SRG proteins, thus promoting grain size. SRG overexpression lines produced more tillers and significantly larger and heavier grains to increase 1,000-grain weight, suggesting that SRG has potential to increase grain yield. Our study indicated that SRG is a new BR responsive factor and BR might regulate grain size by influencing the expression of SRG.

First note of QTL mapping of low vigor traits using the updated F2 'Koroneiki' linkage map of olive

The olive tree (Olea europaea L.), which characterizes the agriculture of the Mediterranean basin, faces challenges adapting to high-density orchards and mechanized cultivation. This study addresses a key issue: controlling tree size to enhance efficiency and manageability in olive cultivation. Utilizing genetic mapping methods, we have identified significant Quantitative Trait Loci (QTL) and candidate genes associated with low-vigor traits in olive trees. Our research on the 'Koroneiki' F2 progeny, which exhibits low vigor traits but remains underutilized in breeding programs, has pinpointed a QTL linked to trunk basal diameter-a trait correlated with plant height based on morphological measurements. Results underscore a strong genetic control of these traits, with a consistent correlation observed over time. We identified two candidate genes - Acid Phosphatase 1, Shikimate O-hydroxycinnamoyltransferase, and a SNP Marker likely associated with Calcium Responsive Proteins - each potentially interacting with plant hormones to influence growth. Controlling olive tree size presents several challenges, including the genetic complexity of polygenic traits like size and vigor, and limited rootstock options. By integrating reference genomes with our genetic analysis, we offer a conceptual advancement that could substantially accelerate breeding timelines compared to traditional approaches. Although genome editing is still a future possibility due to the complexity of olive genetics and the species' recalcitrance to transformation, our study lays a foundational understanding to guide future breeding programs. By targeting the identified candidate genes, this research represents a pivotal step toward selecting new low-vigor genotypes and rootstocks, contributing to innovations in olive cultivation.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development. Hormonal signaling and the maintenance of ROS homeostasis are interconnected, playing indispensable roles in growth, development, and stress responses and orchestrating diverse molecular responses during environmental adversities. Nine principal classes of phytohormones have been categorized: auxins, brassinosteroids, cytokinins, and gibberellins primarily oversee developmental growth regulation, while abscisic acid, ethylene, jasmonic acid, salicylic acid, and strigolactones are the main orchestrators of environmental stress responses. Coordination between phytohormones and transcriptional regulation is crucial for effective plant responses, especially in drought stress. Understanding the interplay of ROS and phytohormones is pivotal for elucidating the molecular mechanisms involved in plant stress responses. This review provides an overview of the intricate relationship between ROS, redox metabolism, and the nine different phytohormones signaling in plants, shedding light on potential strategies for enhancing drought tolerance for sustainable crop production.

Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment

Introduction

Rice samples exposed to the space environment have generated diverse phenotypic variations. Miniature-inverted-repeat transposable elements (MITEs), often found adjacent to genes, play a significant role in regulating the plant genome. Herein, the contribution of MITEs in regulating space-mutagenic phenotypes was explored.

Methods

The space-mutagenic phenotype changes in the F3 to F5 generations of three space-mutagenic lines from the rice varieties Dongnong423 (DN423) and Dongnong (DN416) were meticulously traced. Rice leaves samples at the heading stage from three space-mutagenic lines were subjected to high coverage whole-genome bisulfite sequencing and whole-genome sequencing. These analyses were conducted to investigate the effects of MITEs related epigenetic and genetic variations on space-mutagenic phenotypes.

Results and discussion

Studies have indicated that MITEs within gene regulatory regions might contribute to the formation and differentiation of space-mutagenic phenotypes. The space environment has been shown to induce the transposable elements insertion polymorphisms of MITEs (MITEs-TIPs), with a notable preference for insertion near genes involved in stress response and phenotype regulation. The space-induced MITEs-TIPs contributed to the formation of space-mutagenic phenotype by modulating the expression of gene near the insertion site. This study underscored the pivotal role of MITEs in modulating plant phenotypic variation induced by the space environment, as well as the transgenerational stability of these phenotypic variants.

The OsMAPK6-OsWRKY72 module positively regulates rice leaf angle through brassinosteroid signals

Leaf angle is a major agronomic trait that determines plant architecture, which directly affects rice planting density, photosynthetic efficiency, and yield. The plant phytohormones brassinosteroids (BRs) and the MAPK signaling cascade are known to play crucial roles in regulating leaf angle, but the underlying molecular mechanisms are not fully understood. Here, we report a rice WRKY family transcription factor gene, OsWRKY72, which positively regulates leaf angle by affecting lamina joint development and BR signaling. Phenotypic analysis showed that oswrky72 mutants have smaller leaf angles and exhibit insensitivity to exogenous BRs, whereas OsWRKY72 overexpression lines show enlarged leaf angles and are hypersensitive to exogenous BRs. Histological sections revealed that the change in leaf inclination is due to asymmetric cell proliferation and growth at the lamina joint. Further investigation showed that OsWRKY72 binds directly to the promoter region of BR receptor kinase (OsBRI1), a key gene in the BR signaling pathway, and activates its expression to positively regulate rice BR signaling. In addition, we discovered that OsWRKY72 interacts with and is phosphorylated by OsMAPK6, and this phosphorylation event can enhance OsWRKY72 activity in promoting OsBRI1 expression. Genetic evidence confirmed that OsMAPK6, OsWRKY72, and OsBRI1 function in a common pathway to regulate leaf angle. Collectively, our findings clarify the critical role of the OsWRKY72 transcription factor in regulating rice leaf angle. These results provide valuable insights into the molecular regulatory networks that govern plant architecture in rice.

The brassinosteroid signaling-related ILI-OsAIF-OsbHLH92 transcription factor module antagonistically controls leaf angle and grain size in rice

Atypical basic helix-loop-helix (bHLH) transcription factors, which lack the basic region for DNA binding, are important elements of brassinosteroid (BR) signaling. Recently, our systematic characterization of the rice (Oryza sativa) INCREASED LEAF INCLINATION (ILI) subfamily of atypical bHLHs revealed their indispensable roles in BR-mediated growth and development. Here, we reported the isolation of two additional rice ILI-interacting atypical bHLHs, ATBS1-INTERACTING FACTOR 1 (OsAIF1)/OsbHLH176 and OsAIF2/OsbHLH178. Genetic and cytological analyses of the OsAIFs knockout mutants and overexpression lines revealed that OsAIF1 and OsAIF2 negatively regulate rice leaf inclination and grain size in a synergistic and redundant manner. Compared to the wild-type, osaif knockout mutants exhibited hypersensitivity to BR, while OsAIF1 and OsAIF2 overexpression lines showed greatly reduced sensitivity or complete insensitivity to BR, indicating that these two OsAIFs act as major negative regulators of rice BR signaling. As ILI-interacting negative atypical HLHs, OsAIF1 and OsAIF2 genetically counteracted the positive ILI subfamily of atypical HLHs. Moreover, OsAIF1 and OsAIF2 physically interacted with and antagonized OsbHLH92, a positive regulator of BR signaling, thereby modulating rice development and gene transcription. These findings suggested that the atypical HLHs (ILIs and OsAIF1/OsAIF2) and the bHLH (OsbHLH92) transcription factors form a triantagonistic cascade in rice, counteracting each other to fine-tune leaf angle and grain size through BR signaling. Our results provide insights into the mechanisms balancing BR signaling and growth in rice.

Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa)

INTRODUCTION

Rice (Oryza sativa L.), a staple food for billions worldwide, is challenged by salt stress. Owing to the limited understanding of the physiological and genetic basis of rice salt tolerance, few genes have been identified as valuable in rice breeding, causing a major bottleneck in the development of high-yield, salt-tolerant rice varieties.

OBJECTIVE

This study aims to identify salt tolerance genes/quantitative trait loci (QTLs) with breeding potential in rice.

METHODS

Field trials were conducted with 166 Chinese rice cultivars from saline-affected regions and 412 global rice accessions to assess salt tolerance. Genome-wide association study (GWAS) was performed to identify key loci related to high yield and salt tolerance. Additionally, the impact of introducing beneficial haplotypes on grain yield and salt tolerance was assessed.

RESULTS

The optimal rice plant height of 100-120 cm was crucial for sustaining high yield under both normal and salt stress conditions. GWAS revealed 6 novel QTLs/genes associated with rice plant growth and grain yield across various environments, distinct from previously recognized salt stress-related genes. Notably, the gene PHS10.1, encoding a serine/threonine protein kinase, may regulate carbon metabolism, starch and sucrose metabolism, influencing plant growth and grain yield. Certain haplotypes of the genes regulating plant height and grain yield, including SD1, Ghd7.1, GH3.5, and PHS10.1, were selected in traditional breeding. Moreover, optimizing plant height through the introgression of beneficial alleles of these genes increased grain yield in recipient lines under both normal and saline conditions.

CONCLUSION

We propose that utilizing beneficial haplotypes to optimize plant height can effectively balance the growth-stress trade-offs in rice plants. This represents a promising breeding strategy for the development of crop varieties that are both high-yielding and salt-tolerant.

Untargeted mutagenesis of brassinosteroid receptor SbBRI1 confers drought tolerance by altering phenylpropanoid metabolism in Sorghum bicolor

Drought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID-INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP-seq), we show that the sorghum BRI1-EMS-SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G-box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1-mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought.

Detection of QTLs regulating the second internode length in rice dwarf mutant d1

Stem length is a crucial agronomic trait in rice breeding. The short stature of rice dwarf mutants is caused by shortening of internodes, resulting in five distinct internode elongation patterns: dn, dm, d6, nl and sh. Several genetic studies have been conducted; however, the genetic mechanisms underlying these internode elongation patterns remain unclear. In this study, we examined two Daikoku dwarf (d1) mutants, T65(d1-1) and Kin(d1-7), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65(d1-1) exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin(d1-7) shows a dn-type pattern with a relatively elongated second internode. To identify the genetic factors influencing these phenotypes, we conducted a quantitative trait locus (QTL) analysis using two F2 populations derived from reciprocal crosses between them. The QTL analysis showed that the second internode length is regulated by three QTLs on chromosomes 4, 5, and 6. Epistatic effects were observed through the analysis of F3 progenies, indicating that the combination of Kin(d1-7) alleles at these QTLs is associated with an increased second internode length. Furthermore, specific combinations of alleles result in varying degrees of elongation in the second internode, significantly impacting the internode elongation pattern. These findings contribute to a deeper understanding of the genetic factors influencing the internode elongation patterns in rice.

Functions and Mechanisms of Brassinosteroids in Regulating Crop Agronomic Traits

Brassinosteroids (BRs) perform crucial functions controlling plant growth and developmental processes, encompassing many agronomic traits in crops. Studies of BR-related genes involved in agronomic traits have suggested that BRs could serve as a potential target for crop breeding. Given the pleiotropic effect of BRs, a systematic understanding of their functions and molecular mechanisms is conducive for application in crop improvement. Here, we summarize the functions and underlying mechanisms by which BRs regulate the several major crop agronomic traits, including plant architecture, grain size, as well as the specific trait of symbiotic nitrogen fixation in legume crops. For plant architecture, we discuss the roles of BRs in plant height, branching number and leaf erectness, and propose how progress in these fields may contribute to designing crops with optimal agronomic traits and improved grain yield by accurately modifying BR levels and signaling pathways.

Bona Fide Plant Steroid Receptors are Innovated in Seed Plants and Angiosperms through Successive Whole-Genome Duplication Events

Whole-genome duplication (WGD) events are widespread in plants and animals, thus their long-term evolutionary contribution has long been speculated, yet a specific contribution is difficult to verify. Here, we show that ɛ-WGD and ζ-WGD contribute to the origin and evolution of bona fide brassinosteroid (BR) signaling through the innovation of active BR biosynthetic enzymes and active BR receptors from their respective ancestors. We found that BR receptors BRI1 (BR INSENSITIVE 1) and BRL1/3 (BRI1-LIKES 1/3) derived by ɛ-WGD and ζ-WGD, which occurred in the common ancestor of angiosperms and seed plants, respectively, while orphan BR receptor BRL2 first appeared in stomatophytes. Additionally, CYP85A enzymes synthesizing the bioactive BRs derived from a common ancestor of seed plants, while its sister enzymes CYP90 synthesizing BR precursors presented in all land plants, implying possible ligand-receptor coevolution. Consistently, the island domains (IDs) responsible for BR perception in BR receptors were most divergent among different receptor branches, supporting ligand-driven evolution. As a result, BRI1 was the most diversified BR receptor in angiosperms. Importantly, relative to the BR biosynthetic DET2 gene presented in all land plants, BRL2, BRL1/3 and BRI1 had high expression in vascular plants ferns, gymnosperms and angiosperms, respectively. Notably, BRI1 is the most diversified BR receptor with the most abundant expression in angiosperms, suggesting potential positive selection. Therefore, WGDs initiate a neofunctionalization process diverged by ligand-perception and transcriptional expression, which might optimize both BR biosynthetic enzymes and BR receptors, likely contributing to the evolution of land plants, especially seed plants and angiosperms.

The rice R2R3 MYB transcription factor FOUR LIPS connects brassinosteroid signaling to lignin deposition and leaf angle

Leaf angle is an important agronomic trait for crop architecture and yield. In rice (Oryza sativa), the lamina joint is a unique structure connecting the leaf blade and sheath that determines leaf angle. Brassinosteroid (BR) signaling involving GLYCOGEN SYNTHASE KINASE-3 (GSK3)/SHAGGY-like kinases and BRASSINAZOLE-RESISTANT1 (BZR1) has a central role in regulating leaf angle in rice. In this study, we identified the atypical R2R3-MYB transcription factor FOUR LIPS (OsFLP), the rice homolog of Arabidopsis (Arabidopsis thaliana) AtFLP, as a participant in BR-regulated leaf angle formation. The spatiotemporal specificity of OsFLP expression in the lamina joint was closely associated with lignin deposition in vascular bundles and sclerenchyma cells. OsFLP mutation caused loose plant architecture with droopy flag leaves and hypersensitivity to BRs. OsBZR1 directly targeted OsFLP, and OsFLP transduced BR signals to lignin deposition in the lamina joint. Moreover, OsFLP promoted the transcription of the phenylalanine ammonia-lyase family genes OsPAL4 and OsPAL6. Intriguingly, OsFLP feedback regulated OsGSK1 transcription and OsBZR1 phosphorylation status. In addition, an Ala-to-Thr substitution within the OsFLP R3 helix-turn-helix domain, an equivalent mutation to that in Osflp-1, affected the DNA-binding ability and transcriptional activity of OsFLP. Our results reveal that OsFLP functions with OsGSK1 and OsBZR1 in BR signaling to maintain optimal leaf angle by modulating the lignin deposition in mechanical tissues of the lamina joint.

RMD and Its Suppressor MAPK6 Control Root Circumnutation and Obstacle Avoidance via BR Signaling

Helical growth of the root tip (circumnutation) that permits surface exploration facilitates root penetration into soil. Here, we reveal that rice actin-binding protein RMD aids in root circumnutation, manifested by wavy roots as well as compromised ability to efficiently explore and avoid obstacles in rmd mutants. We demonstrate that root circumnutation defects in rmd depend on brassinosteroid (BR) signaling, which is elevated in mutant roots. Suppressing BR signaling via pharmacological (BR inhibitor) or genetic (knockout of BR biosynthetic or signaling components) manipulation rescues root defects in rmd. We further reveal that mutations in MAPK6 suppress BR signaling and restore normal root circumnutation in rmd, which may be mediated by the interaction between MAPK6, MAPKK4 and BR signaling factor BIM2. Our study thus demonstrates that RMD and MAPK6 control root circumnutation by modulating BR signaling to facilitate early root growth.

BLA1 Affects Leaf Angles by Altering Brassinosteroid Biosynthesis in Rice (Oryza sativa L.)

Brassinosteroids (BRs) are crucial plant hormones influencing diverse developmental processes in rice. While several enzymes in BR biosynthesis have been identified, their regulatory mechanisms remain largely unknown. This study highlights a novel regulatory pathway wherein the CHD3 chromatin remodeler, BLA1, epigenetically modulates the expression of key BR biosynthesis genes, BRD1 and D2. Phenotypic analysis of bla1 mutants revealed significant alterations, such as increased leaf angles and longer mesocotyls, which were alleviated by BR synthesis inhibitors. Moreover, the bla1 mutants showed elevated BR levels that correlated with the significant upregulation of the expression levels of BRD1 and D2, particularly at the lamina joint sites. Mechanistically, the yeast one-hybrid and chromatin immunoprecipitation assays revealed specific binding of BLA1 to the promoter regions of BRD1 and D2, accompanied by a marked enrichment of the transcriptionally active histone modification, H3K4me3, on these loci in the bla1 mutant. Functional assessments of the brd1 and d2 mutants confirmed their reduced sensitivity to BR, further underscoring their critical regulatory roles in BR-mediated developmental processes. Our findings uncovered an epigenetic mechanism that governs BR biosynthesis and orchestrates the expression of BRD1 and D2 to modulate BR levels and influence rice growth and development.

A distinct protein posttranslational modifications-linked OsATL32-OsPPKL2-OsGSK2 loop modulates rice immunity against blast disease

Protein posttranslational modifications play crucial roles in plant immunity through modulating a complicated signaling network mediated by different hormones. We previously demonstrated that OsATL32, an ATL-type E3 ligase, negatively contributes to rice immunity against Magnaporthe oryzae. Here, we show that OsATL32 forms a loop with OsPPKL2 and OsGSK2 through distinct protein posttranslational modifications to modulate rice immunity. OsATL32 ubiquitinates OsPPKL2, a protein phosphatase with Kelch-like repeat domains that exerts positive roles in regulating rice immunity against M. oryzae and chitin-triggered immune responses, for degradation. The glycogen synthase kinase 2 (OsGSK2), which acts as a negative regulator of rice immunity against M. oryzae and chitin-triggered immune responses, phosphorylates OsATL32 to elevate its protein stability and E3 ligase activity on OsPPKL2. Moreover, OsPPKL2 directly dephosphorylates OsGSK2, affecting its kinase activity on substrates including OsATL32 for phosphorylation. Like OsGSK2 as a BR signaling repressor, OsATL32 negatively regulates BR signaling; conversely, OsPPKL2 plays a positive role in BR signaling. These findings provide a molecular mechanism in which OsATL32 serves as a node connecting BR signaling and immunity by associating with OsPPKL2 and OsGSK2, assembling into a distinct protein posttranslational modifications-linked loop that functions in rice BR signaling and immunity.

Global Characterization of DNA Methylation during Rice Leaf Angle Development

During plant development and growth, genomic DNA accumulates chemical markers that determine the levels of gene expression. DNA methylation is an important epigenetic marker involved in plant developmental events. However, the characterization of the role of DNA methylation in rice leaf angle development has lagged behind. Herein, we performed bisulfite sequencing to characterize DNA methylation sites and performed transcriptome and small RNA sequencing during leaf angle development. The results revealed a global reduction in CG methylation during leaf angle establishment. A reduction in gene body CG methylation appears to play a vital role in leaf angle development. The hypomethylated and weakly expressed genes were functionally enriched in the brassinosteroid and auxin signaling pathways. Additionally, the main DNA methyltransferases were inactive. The addition of exogenous DNA methylation inhibitor 5-azacytidine increased the leaf angle, which confirmed that DNA methylation is crucial for leaf angle development. This study revealed a gradual decrease in 24-nucleotide siRNA levels during leaf angle development, particularly in relation to the enrichment of 24-nucleotide siRNAs at different hypomethylated regions that induce leaf angle inclination. Our results indicate crucial roles for DNA methylation in the rice leaf angle developmental stages.

Characterization of flag leaf morphology identifies a major genomic region controlling flag leaf angle in the US winter wheat (Triticum aestivum L.)

KEY MESSAGE

Multi-environmental characterization of flag leaf morphology traits in the US winter wheat revealed nine stable genomic regions for different flag leaf-related traits including a major region governing flag leaf angle. Flag leaf in wheat is the primary contributor to accumulating photosynthetic assimilates. Flag leaf morphology (FLM) traits determine the overall canopy structure and capacity to intercept the light, thus influencing photosynthetic efficiency. Hence, understanding the genetic control of these traits could be useful for breeding desirable ideotypes in wheat. We used a panel of 272 accessions from the hard winter wheat (HWW) region of the USA to investigate the genetic architecture of five FLM traits including flag leaf length (FLL), width (FLW), angle (FLANG), length-width ratio, and area using multilocation field experiments. Multi-environment GWAS using 14,537 single-nucleotide polymorphisms identified 36 marker-trait associations for different traits, with nine being stable across environments. A novel and major stable region for FLANG (qFLANG.1A) was identified on chromosome 1A accounting for 9-13% variation. Analysis of spatial distribution for qFLANG.1A in a set of 2354 breeding lines from the HWW region showed a higher frequency of allele associated with narrow leaf angle. A KASP assay was developed for allelic discrimination of qFLANG.1A and was used for its independent validation in a diverse set of spring wheat accessions. Furthermore, candidate gene analysis for two regions associated with FLANG identified seven putative genes of interest for each of the two regions. The present study enhances our understanding of the genetic control of FLM in wheat, particularly FLANG, and these results will be useful for dissecting the genes underlying canopy architecture in wheat facilitating the development of climate-resilient wheat varieties.

OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice

Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.

Molecular Lesions in BRI1 and Its Orthologs in the Plant Kingdom

Brassinosteroids (BRs) are an essential group of plant hormones regulating numerous aspects of plant growth, development, and stress responses. BRI1, along with its co-receptor BAK1, are involved in brassinosteroid sensing and early events in the BR signal transduction cascade. Mutational analysis of a particular gene is a powerful strategy for investigating its biochemical role. Molecular genetic studies, predominantly in Arabidopsis thaliana, but progressively in numerous other plants, have identified many mutants of the BRI1 gene and its orthologs to gain insight into its structure and function. So far, the plant kingdom has identified up to 40 bri1 alleles in Arabidopsis and up to 30 bri1 orthologs in different plants. These alleles exhibit phenotypes that are identical in terms of development and growth. Here, we have summarized bri1 alleles in Arabidopsis and its orthologs present in various plants including monocots and dicots. We have discussed the possible mechanism responsible for the specific allele. Finally, we have briefly debated the importance of these alleles in the research field and the agronomically valuable traits they offer to improve plant varieties.

Characterization of the ddt1 Mutant in Rice and Its Impact on Plant Height Reduction and Water Use Efficiency

Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world's population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant's improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement.

The TaSnRK1-TabHLH489 module integrates brassinosteroid and sugar signalling to regulate the grain length in bread wheat

Regulation of grain size is a crucial strategy for improving the crop yield and is also a fundamental aspect of developmental biology. However, the underlying molecular mechanisms governing grain development in wheat remain largely unknown. In this study, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor, TabHLH489, which is tightly associated with grain length through genome-wide association study and map-based cloning. Knockout of TabHLH489 and its homologous genes resulted in increased grain length and weight, whereas the overexpression led to decreased grain length and weight. TaSnRK1α1, the α-catalytic subunit of plant energy sensor SnRK1, interacted with and phosphorylated TabHLH489 to induce its degradation, thereby promoting wheat grain development. Sugar treatment induced TaSnRK1α1 protein accumulation while reducing TabHLH489 protein levels. Moreover, brassinosteroid (BR) promotes grain development by decreasing TabHLH489 expression through the transcription factor BRASSINAZOLE RESISTANT1 (BZR1). Importantly, natural variations in the promoter region of TabHLH489 affect the TaBZR1 binding ability, thereby influencing TabHLH489 expression. Taken together, our findings reveal that the TaSnRK1α1-TabHLH489 regulatory module integrates BR and sugar signalling to regulate grain length, presenting potential targets for enhancing grain size in wheat.

Modulation of histone acetylation enables fully mechanized hybrid rice breeding

Hybrid rice has achieved high grain yield and greatly contributes to food security, but the manual-labour-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, the use of small-grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest is promising. However, it is difficult to find ideal grain-size genes for breeding ideal small-grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the use of small-grain alleles of the ideal grain-size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain-size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops.

Major quantitative trait locus qLA3.1 is related to tomato leaf angle by regulating cell length at the petiole base

KEY MESSAGE

qLA3.1, controlling leaf angle in tomato, was fine-mapped to an interval of 4.45 kb on chromosome A03, and one gene encoding auxin response factor was identified as a candidate gene. Leaf angle is a crucial trait in plant architecture that plays an important role in achieving optimal plant structure. However, there are limited reports on gene localization, cloning, and the function of plant architecture in horticultural crops, particularly regarding leaf angle. In this study, we selected 'Z3' with erect leaves and 'Heinz1706' with horizontal leaves as the phenotype and cytological observation. We combined bulked segregant analysis and fine genetic mapping to identify a candidate gene, known as, i.e., qLA3.1, which was related to tomato leaf angle. Through multiple analyses, we found that Solyc03g113410 was the most probably candidate for qLA3.1, which encoded the auxin response factor SlARF11 in tomato and was homologous to OsARF11 related to leaf angle in rice. We discovered that silencing SlARF11 resulted in upright leaves, while plants with over-expressed SlARF11 exhibited horizontal leaves. We also found that cultivars with erect leaves had a mutation from base G to base A. Moreover, quantitative analysis of plants treated with hormones indicated that SlARF11 might participate in cell elongation and the activation of genes related to auxin and brassinosteroid pathways. Transcriptome analysis further validated that SlARF11 may regulate leaf angle through hormone signaling pathways. These data support the idea that the auxin response factor SlARF11 may have an important function in tomato leaf petiole angles.

Molecular mechanism of brassinosteroids involved in root gravity response based on transcriptome analysis

BACKGROUND

Brassinosteroids (BRs) are a class of phytohormones that regulate a wide range of developmental processes in plants. BR-associated mutants display impaired growth and response to developmental and environmental stimuli.

RESULTS

Here, we found that a BR-deficient mutant det2-1 displayed abnormal root gravitropic growth in Arabidopsis, which was not present in other BR mutants. To further elucidate the role of DET2 in gravity, we performed transcriptome sequencing and analysis of det2-1 and bri1-116, bri1 null mutant allele. Expression levels of auxin, gibberellin, cytokinin, and other related genes in the two mutants of det2-1 and bri1-116 were basically the same. However, we only found that a large number of JAZ (JASMONATE ZIM-domain) genes and jasmonate synthesis-related genes were upregulated in det2-1 mutant, suggesting increased levels of endogenous JA.

CONCLUSIONS

Our results also suggested that DET2 not only plays a role in BR synthesis but may also be involved in JA regulation. Our study provides a new insight into the molecular mechanism of BRs on the root gravitropism.

The chromosome-level assembly of the wild diploid alfalfa genome provides insights into the full landscape of genomic variations between cultivated and wild alfalfa

Alfalfa (Medicago sativa L.) is one of the most important forage legumes in the world, including autotetraploid (M. sativa ssp. sativa) and diploid alfalfa (M. sativa ssp. caerulea, progenitor of autotetraploid alfalfa). Here, we reported a high-quality genome of ZW0012 (diploid alfalfa, 769 Mb, contig N50 = 5.5 Mb), which was grouped into the Northern group in population structure analysis, suggesting that our genome assembly filled a major gap among the members of M. sativa complex. During polyploidization, large phenotypic differences occurred between diploids and tetraploids, and the genetic information underlying its massive phenotypic variations remains largely unexplored. Extensive structural variations (SVs) were identified between ZW0012 and XinJiangDaYe (an autotetraploid alfalfa with released genome). We identified 71 ZW0012-specific PAV genes and 1296 XinJiangDaYe-specific PAV genes, mainly involved in defence response, cell growth, and photosynthesis. We have verified the positive roles of MsNCR1 (a XinJiangDaYe-specific PAV gene) in nodulation using an Agrobacterium rhizobia-mediated transgenic method. We also demonstrated that MsSKIP23_1 and MsFBL23_1 (two XinJiangDaYe-specific PAV genes) regulated leaf size by transient overexpression and virus-induced gene silencing analysis. Our study provides a high-quality reference genome of an important diploid alfalfa germplasm and a valuable resource of variation landscape between diploid and autotetraploid, which will facilitate the functional gene discovery and molecular-based breeding for the cultivars in the future.

Transcription factor OsWRKY72 controls rice leaf angle by regulating LAZY1-mediated shoot gravitropism

Leaf angle is a major trait of ideal architecture, which is considered to influence rice (Oryza sativa) cultivation and grain yield. Although a few mutants with altered rice leaf inclination angles have been reported, the underlying molecular mechanism remains unclear. In this study, we showed that a WRKY transcription factor gene, OsWRKY72, was highly expressed in the leaf sheath and lamina joint. Phenotypic analyses showed that oswrky72 mutants had smaller leaf angles than the wild type, while OsWRKY72 overexpression lines exhibited an increased leaf angle. This observation suggests that OsWRKY72 functions as a positive regulator, promoting the enlargement of the leaf angle. Our bioinformatics analysis identified LAZY1 as the downstream gene of OsWRKY72. Electrophoretic mobility shift assays and dual-luciferase analysis revealed that OsWRKY72 directly inhibited LAZY1 by binding to its promoter. Moreover, knocking out OsWRKY72 enhanced shoot gravitropism, which contrasted with the phenotype of lazy1 plants. These results imply that OsWRKY72 regulates the leaf angle through gravitropism by reducing the expression of LAZY1. In addition, OsWRKY72 could directly regulate the expression of other leaf angle-related genes such as FLOWERING LOCUS T-LIKE 12 (OsFTL12) and WALL-ASSOCIATED KINASE 11 (OsWAK11). Our study indicates that OsWRKY72 contributes positively to the expansion of the leaf angle by interfering with shoot gravitropism in rice.

Brassinosteroid-dependent phosphorylation of PHOSPHATE STARVATION RESPONSE2 reduces its DNA-binding ability in rice

Brassinosteroids (BRs) are widely used as plant growth regulators in modern agriculture. Understanding how BRs regulate nutrient signaling is crucial for reducing fertilizer usage. Here we elucidate that the central BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 (GSK2) interacts directly with and phosphorylates PHOSPHATE STARVATION RESPONSE2 (OsPHR2), the key regulator of phosphate (Pi) signaling, to suppress its transcription factor activity in rice (Oryza sativa). We identify a critical phosphorylation site at serine residue S269 of OsPHR2 and demonstrate that phosphorylation by GSK2 or phosphor-mimic mutation of S269 substantially impairs the DNA-binding activity of OsPHR2, and thus diminishes expression of OsPHR2-induced genes and reduces Pi levels. Like BRs, Pi starvation noticeably induces GSK2 instability. We further show that this site-specific phosphorylation event is conserved in Arabidopsis (Arabidopsis thaliana), but varies among the PHR-family members, being present only in most land plants. These results unveil a distinctive post-transcriptional regulatory mechanism in Pi signaling by which BRs promote Pi acquisition, with a potential contribution to the environmental adaptability of plants during their evolution.

Brassinosteroid decreases cadmium accumulation via regulating gibberellic acid accumulation and Cd fixation capacity of root cell wall in rice (Oryza sativa)

The precise mechanism behind the association between plants' reactions to cadmium (Cd) stress and brassinosteroid (BR) remains unclear. In the current investigation, Cd stress quickly increased the endogenous BR concentration in the rice roots. Exogenous BR also increased the hemicellulose level in the root cell wall, which in turn increased its capacity to bind Cd. Simultaneously, the transcription level of genes responsible for root Cd absorption was decreased, including Natural Resistance-Associated Macrophage Protein 1/5 (OsNRAMP1/5) and a major facilitator superfamily gene called OsCd1. Ultimately, the increased expression of Heavy Metal ATPase 3 (OsHMA3) and the decreased expression of OsHMA2, which was in charge of separating Cd into vacuoles and translocating Cd to the shoots, respectively, led to a decrease in the amount of Cd that accumulated in the rice shoots. In contrast, transgenic rice lines overexpressing OsGSK2 (a negative regulator in BR signaling) accumulated more Cd, while OsGSK2 RNA interference (RNAi) rice line accumulated less Cd. Furthermore, BR increased endogenous Gibberellic acid (GA) level, and applying GA could replicate its alleviative effect. Taken together, BR decreased Cd accumulation in rice by mediating the cell wall's fixation capacity to Cd, which might relied on the buildup of the GA.

Transcriptional Regulation and Gene Mapping of Internode Elongation and Late Budding in the Chinese Cabbage Mutant lcc

Two important traits of Chinese cabbage, internode length and budding time, destroy the maintenance of rosette leaves in the vegetative growth stage and affect flowering in the reproductive growth stage. Internodes have received much attention and research in rice due to their effect on lodging resistance, but they are rarely studied in Chinese cabbage. In Chinese cabbage, internode elongation affects not only the maintenance of rosette leaves but also bolting and yield. Budding is also an important characteristic of Chinese cabbage entering reproductive growth. Although many studies have reported on flowering and bolting, studies on bud emergence and the timing of budding are scarce. In this study, the mutant lcc induced by EMS (Ethyl Methane Sulfonate) was used to study internode elongation in the seedling stage and late budding in the budding stage. By comparing the gene expression patterns of mutant lcc and wild-type A03, 2280 differentially expressed genes were identified in the seedling stage, 714 differentially expressed genes were identified in the early budding stage, and 1052 differentially expressed genes were identified in the budding stage. Here, the transcript expression patterns of genes in the plant hormone signaling and clock rhythm pathways were investigated in relation to the regulation of internode elongation and budding in Chinese cabbage. In addition, an F2 population was constructed with the mutants lcc and R500. A high-density genetic map with 1602 marker loci was created, and QTLs for internode length and budding time were identified. Specifically, five QTLs for internode length and five QTLs for budding time were obtained. According to transcriptome data analysis, the internode length candidate gene BraA02g005840.3C (PIN8) and budding time candidate genes BraA02g003870.3C (HY5-1) and BraA02g005190.3C (CHS-1) were identified. These findings provide insight into the regulation of internode length and budding time in Chinese cabbage.

OsWRKY78 regulates panicle exsertion via gibberellin signaling pathway in rice

Panicle exsertion is one of the crucial agronomic traits in rice (Oryza sativa). Shortening of panicle exsertion often leads to panicle enclosure and severely reduces seed production. Gibberellin (GA) plays important roles in regulating panicle exsertion. However, the underlying mechanism and the relative regulatory network remain elusive. Here, we characterized the oswrky78 mutant showing severe panicle enclosure, and found that the defect of oswrky78 is caused by decreased bioactive GA contents. Biochemical analysis demonstrates that OsWRKY78 can directly activate GA biosynthesis and indirectly suppress GA metabolism. Moreover, we found OsWRKY78 can interact with and be phosphorylated by mitogen-activated protein kinase (MAPK) kinase OsMAPK6, and this phosphorylation can enhance OsWRKY78 stability and is necessary for its biological function. Taken together, these results not only reveal the critical function of OsWRKY78, but also reveal its mechanism via mediating crosstalk between MAPK and the GA signaling pathway in regulating panicle exsertion.

A mutation in the brassinosteroid biosynthesis gene CpDWF5 disrupts vegetative and reproductive development and the salt stress response in squash (Cucurbita pepo)

A Cucurbita pepo mutant with multiple defects in growth and development has been identified and characterized. The mutant dwfcp displayed a dwarf phenotype with dark green and shrinking leaves, shortened internodes and petioles, shorter but thicker roots and greater root biomass, and reduced fertility. The causal mutation of the phenotype was found to disrupt gene Cp4.1LG17g04540, the squash orthologue of the Arabidopsis brassinosteroid (BR) biosynthesis gene DWF5, encoding for 7-dehydrocholesterol reductase. A single nucleotide transition (G > A) causes a splicing defect in intron 6 that leads to a premature stop codon and a truncated CpDWF5 protein. The mutation co-segregated with the dwarf phenotype in a large BC1S1 segregating population. The reduced expression of CpDWF5 and brassinolide (BL) content in most mutant organs, and partial rescue of the mutant phenotype by exogenous application of BL, showed that the primary cause of the dwarfism in dwfcp is a BR deficiency. The results showed that in C. pepo, CpDWF5 is not only a positive growth regulator of different plant organs but also a negative regulator of salt tolerance. During germination and the early stages of seedling development, the dwarf mutant was less affected by salt stress than the wild type, concomitantly with a greater upregulation of genes associated with salt tolerance, including those involved in abscisic acid (ABA) biosynthesis, ABA and Ca2+ signaling, and those coding for cation exchangers and transporters.

Enhancing rice panicle branching and grain yield through tissue-specific brassinosteroid inhibition

Crop yield potential is constrained by the inherent trade-offs among traits such as between grain size and number. Brassinosteroids (BRs) promote grain size, yet their role in regulating grain number is unclear. By deciphering the clustered-spikelet rice germplasm, we show that activation of the BR catabolic gene BRASSINOSTEROID-DEFICIENT DWARF3 (BRD3) markedly increases grain number. We establish a molecular pathway in which the BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 phosphorylates and stabilizes OsMADS1 transcriptional factor, which targets TERMINAL FLOWER1-like gene RICE CENTRORADIALIS2. The tissue-specific activation of BRD3 in the secondary branch meristems enhances panicle branching, minimizing negative effects on grain size, and improves grain yield. Our study showcases the power of tissue-specific hormonal manipulation in dismantling the trade-offs among various traits and thus unleashing crop yield potential in rice.

Transcriptomic and functional analyzes reveal that the brassinosteroid insensitive 1 receptor (OsBRI1) regulates cold tolerance in rice

Brassinosteroids (BR) play crucial roles in plant development and abiotic stresses in plants. Exogenous application of BR can significantly enhance cold tolerance in rice. However, the regulatory relationship between cold tolerance and the BR signaling pathway in rice remains largely unknown. Here, we characterized functions of the BR receptor OsBRI1 in response to cold tolerance in rice using its loss-of-function mutant (d61-1). Our results showed that mutant d61-1 was less tolerant to cold stress than wild-type (WT). Besides, d61-1 had lower levels than WT for some physiological parameters, including catalase activity (CAT), superoxide dismutase activity (SOD), peroxidase activity (POD), peroxidase activity (PRO), soluble protein, and soluble sugar content, while malondialdehyde content (MDA) and relative electrical conductivity (REC) levels in d61-1 were higher than those in WT plants. These results indicated that the loss of OsBRI1 function resulted in decreased cold tolerance in rice. In addition, we performed RNA sequencing (RNA-seq) of WT and d61-1 mutant under cold stress. Numerous common and unique differentially expressed genes (DEGs) with up- and down-regulation were observed in WT and d61-1 mutant. Some DEGs were expressed to various degrees, even opposite, between CK1 vs. T1 (WT) and CK2 vs. T2 (d61-1). Among these specific DEGs, some typical genes are involved in plant tolerance to cold stress. Through weighted correlation network analysis (WGCNA), 50 hub genes were screened in the turquoise and blue module. Many genes were involved in cold stress and plant hormone, such as Os01g0279800 (BRI1-associated receptor kinase 1 precursor), Os10g0513200 (Dwarf and tiller-enhancing 1, DTE1), Os02g0706400 (MYB-related transcription factor, OsRL3), etc. Differential expression levels of some genes were verified in WT and d61-1 under cold stress using qRT-PCR. These valuable findings and gene resources will be critical for understanding the regulatory relationships between cold stress tolerance and the BR signaling pathways in rice.

Rice ILI atypical bHLH transcription factors antagonize OsbHLH157/OsbHLH158 during brassinosteroid signaling

Brassinosteroids (BRs) are a group of steroid hormones that play crucial roles in plant growth and development. Atypical bHLH transcription factors that lack the basic region for DNA binding have been implicated in BR signaling. However, the underlying mechanisms of atypical bHLHs in regulation of rice (Oryza sativa) BR signaling are still largely unknown. Here, we describe a systematic characterization of INCREASED LEAF INCLINATION (ILI) subfamily atypical bHLH transcription factors in rice. A total of 8 members, ILI1 to ILI8, with substantial sequence similarity were retrieved. Knockout and overexpression analyses demonstrated that these ILIs play unequally redundant and indispensable roles in BR-mediated growth and development in rice, with a more prominent role for ILI4 and ILI5. The ili3/4/5/8 quadruple and ili1/3/4/7/8 quintuple mutants displayed tremendous BR-related defects with severe dwarfism, erect leaves, and sterility. Biochemical analysis showed that ILIs interact with OsbHLH157 and OsbHLH158, which are also atypical bHLHs and have no obvious transcriptional activity. Overexpression of OsbHLH157 and OsbHLH158 led to drastic BR-defective growth, whereas the osbhlh157 osbhlh158 double mutant developed a typical BR-enhanced phenotype, indicating that OsbHLH157 and OsbHLH158 play a major negative role in rice BR signaling. Further transcriptome analyses revealed opposite effects of ILIs and OsbHLH157/OsbHLH158 in regulation of downstream gene expression, supporting the antagonism of ILIs and OsbHLH157/OsbHLH158 in maintaining the balance of BR signaling. Our results provide insights into the mechanism of BR signaling and plant architecture formation in rice.

Regulatory networks of the F-box protein FBX206 and OVATE family proteins modulate brassinosteroid biosynthesis to regulate grain size and yield in rice

F-box proteins participate in the regulation of many processes, including cell division, development, and plant hormone responses. Brassinosteroids (BRs) regulate plant growth and development by activating core transcriptional and other multiple factors. In rice, OVATE family proteins (OFPs) participate in BR signalling and regulate grain size. Here we identified an F-box E3 ubiquitin ligase, FBX206, that acts as a negative factor in BR signalling and regulates grain size and yield in rice. Suppressed expression of FBX206 by RNAi leads to promoted plant growth and increased grain yield. Molecular analyses showed that the expression levels of BR biosynthetic genes were up-regulated, whereas those of BR catabolic genes were down-regulated in FBX206-RNAi plants, resulting in the accumulation of 28-homoBL, one of the bioactive BRs. FBX206 interacted with OsOFP8, a positive regulator in BR signalling, and OsOFP19, a negative regulator in BR signalling. SCFFBX206 mediated the degradation of OsOFP8 but suppressed OsOFP19 degradation. OsOFP8 interacted with OsOFP19, and the reciprocal regulation between OsOFP8 and OsOFP19 required the presence of FBX206. FBX206 itself was ubiquitinated and degraded, but interactions of OsOFP8 and OsOFP19 synergistically suppressed the degradation of FBX206. Genetic interactions indicated an additive effect between FBX206 and OsOFP8 and epistatic effects of OsOFP19 on FBX206 and OsOFP8. Our study reveals the regulatory networks of FBX206, OsOFP8, and OsOFP19 in BR signalling that regulate grain size and yield in rice.

An update on evolutionary, structural, and functional studies of receptor-like kinases in plants

All living organisms must develop mechanisms to cope with and adapt to new environments. The transition of plants from aquatic to terrestrial environment provided new opportunities for them to exploit additional resources but made them vulnerable to harsh and ever-changing conditions. As such, the transmembrane receptor-like kinases (RLKs) have been extensively duplicated and expanded in land plants, increasing the number of RLKs in the advanced angiosperms, thus becoming one of the largest protein families in eukaryotes. The basic structure of the RLKs consists of a variable extracellular domain (ECD), a transmembrane domain (TM), and a conserved kinase domain (KD). Their variable ECDs can perceive various kinds of ligands that activate the conserved KD through a series of auto- and trans-phosphorylation events, allowing the KDs to keep the conserved kinase activities as a molecular switch that stabilizes their intracellular signaling cascades, possibly maintaining cellular homeostasis as their advantages in different environmental conditions. The RLK signaling mechanisms may require a coreceptor and other interactors, which ultimately leads to the control of various functions of growth and development, fertilization, and immunity. Therefore, the identification of new signaling mechanisms might offer a unique insight into the regulatory mechanism of RLKs in plant development and adaptations. Here, we give an overview update of recent advances in RLKs and their signaling mechanisms.

The transcription factor MYB110 regulates plant height, lodging resistance, and grain yield in rice

The high-yielding Green Revolution varieties of cereal crops are characterized by a semidwarf architecture and lodging resistance. Plant height is tightly regulated by the availability of phosphate (Pi), yet the underlying mechanism remains obscure. Here, we report that rice (Oryza sativa) R2R3-type Myeloblastosis (MYB) transcription factor MYB110 is a Pi-dependent negative regulator of plant height. MYB110 is a direct target of PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) and regulates OsPHR2-mediated inhibition of rice height. Inactivation of MYB110 increased culm diameter and bending resistance, leading to enhanced lodging resistance despite increased plant height. Strikingly, the grain yield of myb110 mutants was elevated under both high- and low-Pi regimes. Two divergent haplotypes based on single nucleotide polymorphisms in the putative promoter of MYB110 corresponded with its transcript levels and plant height in response to Pi availability. Thus, fine-tuning MYB110 expression may be a potent strategy for further increasing the yield of Green Revolution cereal crop varieties.

A mutation in CsDWF7 gene encoding a delta7 sterol C-5(6) desaturase leads to the phenotype of super compact in cucumber (Cucumis sativus L.)

KEY MESSAGE

A novel super compact mutant, scp-3, was identified using map-based cloning in cucumber. The CsDWF7 gene encoding a delta7 sterol C-5(6) desaturase was the candidate gene of scp-3. Mining dwarf genes is important in understanding stem growth in crops. However, only a small number of dwarf genes have been cloned or characterized. Here, we characterized a cucumber (Cucumis sativus L.) dwarf mutant, super compact 3 (scp-3), which displays shortened internodes and dark green leaves with a wrinkled appearance. The photosynthetic rate of scp-3 is significantly lower than that of the wild type. The dwarf phenotype of scp-3 mutant can be partially rescued by the exogenous brassinolide (BL) application, and the endogenous brassinosteroids (BRs) levels in the scp-3 mutant were significantly lower compared to the wild type. Microscopic examination revealed that the reduced internode length in scp-3 resulted from a decrease in cell size. Genetic analysis showed that the dwarf phenotype of scp-3 was controlled by a single recessive gene. Combined with bulked segregant analysis and map-based cloning strategy, we delimited scp-3 locus into an 82.5 kb region harboring five putative genes, but only one non-synonymous mutation (A to T) was discovered between the mutant and its wild type in this region. This mutation occurred within the second exon of the CsGy4G017510 gene, leading to an amino acid alteration from Leu156 to His156. This gene encodes the CsDWF7 protein, an analog of the Arabidopsis DWF7 protein, which is known to be involved in the biosynthesis of BRs. The CsDWF7 protein was targeted to the cell membrane. In comparison to the wild type, scp-3 exhibited reduced CsDWF7 expression in different tissues. These findings imply that CsDWF7 is essential for both BR biosynthesis as well as growth and development of cucumber plants.

HvGSK1.1 Controls Salt Tolerance and Yield through the Brassinosteroid Signaling Pathway in Barley

Brassinosteroids (BRs) are a class of plant steroid hormones that are essential for plant growth and development. BRs control important agronomic traits and responses to abiotic stresses. Through the signaling pathway, BRs control the expression of thousands of genes, resulting in a variety of biological responses. The key effectors of the BR pathway are two transcription factors (TFs): BRASSINAZOLE RESISTANT 1 (BZR1) and BRI1-EMSSUPPRESSOR 1 (BES1). Both TFs are phosphorylated and inactivated by the Glycogen synthase kinase 3 BRASSINOSTEROID INSENSITIVE2 (BIN2), which acts as a negative regulator of the BR pathway. In our study, we describe the functional characteristics of HvGSK1.1, which is one of the GSK3/SHAGGY-like orthologs in barley. We generated mutant lines of HvGSK1.1 using CRISPR/Cas9 genome editing technology. Next Generation Sequencing (NGS) of the edited region of the HvGSK1.1 showed a wide variety of mutations. Most of the changes (frameshift, premature stop codon, and translation termination) resulted in the knock-out of the target gene. The molecular and phenotypic characteristics of the mutant lines showed that the knock-out mutation of HvGSK1.1 improved plant growth performance under salt stress conditions and increased the thousand kernel weight of the plants grown under normal conditions. The inactivation of HvGSK1.1 enhanced BR-dependent signaling, as indicated by the results of the leaf inclination assay in the edited lines. The plant traits under investigation are consistent with those known to be regulated by BRs. These results, together with studies of other GSK3 gene members in other plant species, suggest that targeted editing of these genes may be useful in creating plants with improved agricultural traits.

Supplementary Low Far-Red Light Promotes Proliferation and Photosynthetic Capacity of Blueberry In Vitro Plantlets

Far-red light exerts an important regulatory influence on plant growth and development. However, the mechanisms underlying far-red light regulation of morphogenesis and photosynthetic characteristics in blueberry plantlets in vitro have remained elusive. Here, physiological and transcriptomic analyses were conducted on blueberry plantlets in vitro supplemented with far-red light. The results indicated that supplementation with low far-red light, such as 6 μmol m-2 s-1 and 14 μmol m-2 s-1 far-red (6FR and 14FR) light treatments, significantly increased proliferation-related indicators, including shoot length, shoot number, gibberellin A3, and trans-zeatin riboside content. It was found that 6FR and 14 FR significantly reduced chlorophyll content in blueberry plantlets but enhanced electron transport rates. Weighted correlation network analysis (WGCNA) showed the enrichment of iron ion-related genes in modules associated with photosynthesis. Genes such as NAC, ABCG11, GASA1, and Erf74 were significantly enriched within the proliferation-related module. Taken together, we conclude that low far-red light can promote the proliferative capacity of blueberry plantlets in vitro by affecting hormone pathways and the formation of secondary cell walls, concurrently regulating chlorophyll content and iron ion homeostasis to affect photosynthetic capacity.

Leveraging brassinosteroids towards the next Green Revolution

The use of gibberellin-related dwarfing genes significantly increased grain yield during the Green Revolution. Brassinosteroids (BRs) play a vital role in regulating agronomic traits and stress resistance. The potential of BR-related genes in crop improvement has been well demonstrated, positioning BRs as crucial targets for the next agricultural biotechnological revolution. However, BRs exert pleiotropic effects on plants, and thus present both opportunities and challenges for their application. Recent research suggests promising strategies for leveraging BR regulatory molecules for crop improvement, such as exploring function-specific genes, identifying beneficial alleles, inducing favorable mutations, and optimizing spatial hormone distribution. Advancing our understanding of the roles of BRs in plants is imperative to implement these strategies effectively.

Tuning plant phenotypes by precise, graded downregulation of gene expression

The ability to control gene expression and generate quantitative phenotypic changes is essential for breeding new and desired traits into crops. Here we report an efficient, facile method for downregulating gene expression to predictable, desired levels by engineering upstream open reading frames (uORFs). We used base editing or prime editing to generate de novo uORFs or to extend existing uORFs by mutating their stop codons. By combining these approaches, we generated a suite of uORFs that incrementally downregulate the translation of primary open reading frames (pORFs) to 2.5-84.9% of the wild-type level. By editing the 5' untranslated region of OsDLT, which encodes a member of the GRAS family and is involved in the brassinosteroid transduction pathway, we obtained, as predicted, a series of rice plants with varied plant heights and tiller numbers. These methods offer an efficient way to obtain genome-edited plants with graded expression of traits.

A potential candidate gene associated with the angles of the ear leaf and the second leaf above the ear leaf in maize

BACKGROUND

Leaf angle is a key trait for maize plant architecture that plays a significant role in its morphological development, and ultimately impacting maize grain yield. Although many studies have been conducted on the association and localization of genes regulating leaf angle in maize, most of the candidate genes identified are associated with the regulation of ligule-ear development and phytohormone pathways, and only a few candidate genes have been reported to enhance the mechanical strength of leaf midrib and vascular tissues.

RESULTS

To address this gap, we conducted a genome-wide association study (GWAS) using the leaf angle phenotype and genotyping-by-sequencing data generated from three recombinant inbred line (RIL) populations of maize. Through GWAS analysis, we identified 156 SNPs significantly associated with the leaf angle trait and detected a total of 68 candidate genes located within 10 kb upstream and downstream of these individual SNPs. Among these candidate genes, Zm00001d045408, located on chromosome 9 emerged as a key gene controlling the angles of both the ear leaf and the second leaf above the ear leaf. Notably, this new gene's homolog in Arabidopsis promotes cell division and vascular tissue development. Further analysis revealed that a SNP transversion (G/T) at 7.536 kb downstream of the candidate gene Zm00001d045408 may have caused a reduction in leaf angles of the ear and the second leaf above the ear leaf. Our analysis of the 10 kb region downstream of this candidate gene revealed a 4.337 kb solo long-terminal reverse transcription transposon (solo LTR), located 3.112 kb downstream of Zm00001d045408, with the SNP located 87 bp upstream of the solo LTR.

CONCLUSIONS

In summary, we have identified a novel candidate gene, Zm00001d045408 and a solo LTR that are associated with the angles of both the ear leaf and the second leaf above the ear leaf. The future research holds great potential in exploring the precise role of newly identified candidate gene in leaf angle regulation. Functional characterization of this gene can help in gaining deeper insights into the complex genetic pathways underlying maize plant architecture.